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Developer Instructions

Developer-instructions.Rmd

Updating Reference Data for the Database

The Ecotox database is updated quarterly by the US EPA. Updating this database within wqbench involves several steps including downloading the new database, reviewing and updating reference files in the package, and updating and redeploying the shiny app. The process below outlines the steps necessary to update the wqbench package. The instructions to update and redeploy the shinyapp can be found here.

Process

  1. Download (clone or pull) the wqbench repo and open in RStudio. The best practice is to open a new git branch, called something like update-[date-of-new-ecotox]. In Rstudio, git pane -> New branch -> give it a name, and check “Sync branch with remote”.

  2. Ensure you have the most recent copy of the database with the reference files added. To do this, load the package, and run the function wqb_create_data_set():

devtools::load_all()

wqb_create_data_set(
  file_path = "~/Ecotoxicology/ecotox",
  version = 1,
  folder_path = "~/Ecotoxicology/ecotox_db/"
)
  1. Execute the code in the script scripts/review-reference-datasets-01.R.
  • This script will generate and save a set of csv files that need to be reviewed and updated to allow new values through the data cleaning steps.
  • At the top of the script you will need to set the file path for the database and the location to save the files that are generated. By defeault they will save at: "~/Poisson/Data/wqbench/[current-year]/review/to-be-reviewed/"
  1. After the files are generated, they need to be reviewed and updated by a technical expert.
  • The next step must wait until the review is complete.
  • The life stage code file can’t be reviewed until after the trophic groups have been updated.
  1. Once the files are reviewed they should be placed in: "~/Poisson/Data/wqbench/[current-year]/review/completed/"
  • Then run the scripts/update-reference-datasets-01.R script.
  • Run this line by line - You will be shown several displays showing the updates that will be made to the internal data - ensure these look ok. If they do, continue executing the script, if not you will need to revisit your review and the changes you made to the csv files in the completed folder.
  • This will read in the reviewed files and update the reference files in the inst/extdata folder.

  1. The package needs to be re-built for the files to be part of the package. Run devtools::load_all().

  2. Run the wqb_create_data_set() function to create the database with the new reference data.

  3. To review/update the life stage codes, repeat steps 2 through 6 but run scripts/review-reference-datasets-02.R, review the file, and run scripts/update-reference-datasets-02.R.The trophic groups need to be updated before life stage codes can be reviewed.

  4. Run the wqb_create_data_set() function again to create the database with the new reference data.

  5. These steps will have caused changes to several files in inst/extdata. The changes will be shown in the Git pane in RStudio. Commit these files to Git, and push it to GitHub. Go to the GitHub repository, and open a pull request from your branch (created in step 1). Best practice is to have someone review the PR, but if you know the changes are good, you can merge it yourself. At the very least, ensure that all of the automated checks pass before you merge.

    9a. In rare cases, the “Add Data” templates may also need to be updated after the reference files are updated. See the “Update the Add Data Templates article for instructions.

  6. Once your update is merged, install the new version: devtools::install_github("bcgov/wqbench").

Reference File Review Process

Below are instructions for how to fill out and complete each of the reference files.

Concentration Conversion

This data set should be reviewed each time a new version of the database is downloaded.

  • If there is no value in the conc_conversion_flag column this indicates it is a new concentration unit that was not in the previous version of the database.
  • The goal of the review is to ensure all cells in the conc_conversion_flag column are filled in.
    • A zero (0) indicates the concentration cannot be converted to mg/L or ppm.
      • If the units cannot be converted to mg/L or ppm then put a 0 in the row.
      • No additional columns need to be filled in if the unit is given a value of 0 in the conc_conversion_flag column.
    • A one (1) indicates the concentration can be converted to mg/L or ppm.
      • If the units can be converted put a 1 in the row.
        • In the conc_conversion_value_multiplier column fill in the value needed to convert the units into mg/L or ppm.
        • In the conc_conversion_unit column fill in either mg/L or ppm.
    • Once completed, this file should be saved in the "completed" subfolder in the review folder.

If any incorrect conversions are found, then those rows can be updated.

Duration Conversion

This data set should be reviewed each time a new version of the database is downloaded.

  • If there is no value in the duration_units_to_keep column this indicates it is a new concentration unit that was not in the previous version of the database.
  • The goal of the review is to ensure all cells in the duration_units_to_keep column are filled in.
    • A zero (0) indicates the duration cannot be converted to hours.
      • If the units cannot be converted to hours, then put a 0 in the row.
      • No additional columns need to be filled in if the unit is given a value of 0 in the duration_units_to_keep column.
    • A one (1) indicates the duration can be converted to hours.
      • If the units can be converted put a 1 in the row.
        • In the duration_value_multiplier_to_hours column fill in the value needed to convert the units into hours.
        • In the comments column write why the conversion was chosen since there may be an assumption made during the conversion. For example, if converting month into hours are you basing the conversion on 30 or 31 days.
    • Once completed, this file should be saved in the "completed" subfolder in the review folder.

If any incorrect conversions are found, then those rows can be updated.

Trophic Groups

This data set should be reviewed each time a new version of the database is downloaded.

  • Two files will be generated to help review the trophic group data.
    • missing-trophic-group-review.csv
      • This is a summary that shows the unique phylum, class, order, and family of new taxa in the new version of Ecotox database, that do not meet the exclusion criteria. In other words, these are candidate taxa to be added to the internal dataset.
      • This file contains three columns for the reviewer to consider: trophic_group, ecological_group, and exclude_from_db.
        • If the taxon is not appropriate for inclusion, put a 1 in the exclude_from_db column. Otherwise leave it blank.
        • If it is appropriate to include, fill out the trophic_group and ecological_group columns. Valid values for trophic_group are: “Invertebrate”, “Algae”, “Amphibian”, “Plant”, “Bacteria”, “Fish”. Valid values for ecological_group are: “Planktonic Invertebrate”, “Other”, “Salmonid”.
        • If there is a row in the “missing-trophic-review” sheet that doesn’t have family or order, do one of two things: if the phylum/division is really small and/or the whole taxon can be assigned an ecological group and trophic group, do so. If not (e.g. Annelida, Arthropoda), put 1 in the exclude_from_db column so that this phylum/division won’t appear for you to review again, but lower levels within that phylum/division will.
      • Once completed, this file should be saved in the "completed" subfolder in the review folder.
    • species-coded-in-db-ref.csv
      • This is a list of all the species data from the database that have been filtered where organism_habitat is “Water”.
      • This file is for reference and not to be updated or sent back for integration.

Life Stage Codes

This data set should be reviewed each time a new version of the database is downloaded.

This data set will be sent separately after the first round of files is reviewed because this data depends on the updates to the trophic group data. Only fish and amphibian groups need the life stage categorized into simple groups, so this file only contains fish and amphibians.

lifestage-code-review.csv: - If there is no value in the simple_lifestage column this indicates it is a new life stage that was not in the previous coding of the database. - The goal of the review is to ensure all cells in the simple_lifestage are filled in. - In the simple_lifestage column fill in any empty cells with either els (early life stage), juvenile or adult.

Once completed, this file should be saved in the "completed" subfolder in the review folder.

BC Species

This reference dataset has not been included in the review-reference-datasets.R script as it should not vary from year to year.

This data set is a comprehensive list that was generated from B.C. Conservation Data Centre.

Any species that is in ECOTOX, but not listed in the bc-species.csv reference file is treated as not present in BC.

Concentration Endpoints

This reference dataset has not been included in the review-reference-datasets.R script as it should not vary from year to year.

There is a comprehensive list that should not need to be adjusted.

The list of concentration endpoints are generated in the scripts/concentration-endpoints.R script.

If updates are required then update the concentration-endpoints.R script.